The 31-year-old took a blow to his knee during the Magners League win over Ulster in Cardiff a week ago and has been forced to undergo an operation.
Shanklin had to withdraw from the 2009 British & Irish Lions tour through injury last year and now his latest season has been brought to a premature end.
It couldn’t have come at a worse time for the Blues, who are embroiled in a bitter battle for Heineken Cup qualification via their own domestic league – and have to travel to face Newcastle falcons in the quarter-finals of the AMLIN Challenge Cup next week.
Shanklin is set to have surgery on his knee to clean it out and is expected to be out of action for up to eight weeks. If that is the case, he will probably be a non-starter for Wales’ summer tour to New Zealand.